Federal authorities said Thursday's move to seize the assets of the New York-based Alavi Foundation over alleged Iranian ties should not effect the activities of the organization's many tenants, which include mosques in Maryland, New York, Texas, and California.

The forfeiture action, however, is raising concerns about religious freedom among Muslims, many of whom already say government counterterrorism efforts unfairly tarnish the vast majority of law abiding Muslims.

"As a civil rights organization we are concerned that the seizure of American houses of worship could have a chilling effect on the religious freedom of citizens of all faiths and may send a negative message to Muslims worldwide," the Council on American-Islamic Relations (CAIR) said in a statement.

"The American Muslim and faith communities must not allow houses of worship to become pawns in geopolitical struggles," Imam Bray told CNN. "The tension between the United States and Iran must not be played out in the mosques of America."

Others raised concerns that the move may implicate the imams and communities using those mosques, though prosecutors have made it clear they do not accuse the tenants of the Alavi Foundation's properties of any wrongdoing.

The Muslim Public Affairs Council called on federal prosecutors "to avoid indicting entire institutions and mosques, as they play a vital role in their communities."

Government seizure of properties that house religious institutions is a rarity, according to experts. None of the properties have been formally seized yet and the action is likely to be challenged in court.

But without funding from the Alavi Foundation, which has distributed millions of dollars for social services in the Muslim community, many of these Islamic centers will probably close. According to the Associated Press, "Alavi was one of the few central sources of funding for American Shiite communities, which have far fewer resources than US Sunnis."

The government's action against the Alavi Foundation could add to lingering American suspicious about the Muslim community, said others.

"It's also coming at a particularly bad time right now.... American Muslims are concerned about a backlash over the Fort Hood shooting," Basim Elkarra, executive director of the Sacramento Valley chapter of CAIR, told the Sacramento Bee. "And millions of Muslims are going to be gathering in Mecca for the pilgrimage and hearing about the government seizing mosques. It's just coming at a particularly bad time," she added.